1. scAnnotatR
  2. NAMESPACE
Browse code

adapt model download function to use AnnotationHub

nttvy authored on 15/09/2021 21:17:08
Showing 1 changed files
NAMESPACE
History View file @ 1bd749c
... ... 
@@ -17,7 +17,7 @@ export(scAnnotatR)
17 17 
 export(test_classifier)
18 18 
 export(train_classifier)
19 19 
 exportMethods(show)
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-import(BiocFileCache)
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+import(AnnotationHub)
21 21 
 import(ROCR)
22 22 
 import(SingleCellExperiment)
23 23 
 import(ape)
... ... 
@@ -29,7 +29,6 @@ import(ggplot2)
29 29 
 import(kernlab, except = c(alpha, predict))
30 30 
 import(methods)
31 31 
 import(pROC)
32 
-import(tools)
33 32 
 importFrom(Seurat,GetAssayData)
34 33 
 importFrom(Seurat,Idents)
35 34 
 importFrom(SummarizedExperiment,assay)
Browse code

merge separate methods for Seurat and SCE signatures into one function

nttvy authored on 29/07/2021 22:23:02
Showing 1 changed files
NAMESPACE
History View file @ a212ecf
... ... 
@@ -31,6 +31,7 @@ import(methods)
31 31 
 import(pROC)
32 32 
 import(tools)
33 33 
 importFrom(Seurat,GetAssayData)
34 
+importFrom(Seurat,Idents)
34 35 
 importFrom(SummarizedExperiment,assay)
35 36 
 importFrom(SummarizedExperiment,colData)
36 37 
 importFrom(stats,predict)
Browse code

remove default_models store in package, use BiocFileCache to manage pretrained models

Former-commit-id: 4a69d2314d0fe5849d5002a1dc1cdd474f9afaff

nttvy authored on 29/07/2021 14:57:11
Showing 1 changed files
NAMESPACE
History View file @ a5d06e3
... ... 
@@ -6,6 +6,7 @@ export(caret_model)
6 6 
 export(cell_type)
7 7 
 export(classify_cells)
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 export(delete_model)
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+export(load_models)
9 10 
 export(marker_genes)
10 11 
 export(p_thres)
11 12 
 export(parent)
... ... 
@@ -16,6 +17,7 @@ export(scAnnotatR)
16 17 
 export(test_classifier)
17 18 
 export(train_classifier)
18 19 
 exportMethods(show)
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+import(BiocFileCache)
19 21 
 import(ROCR)
20 22 
 import(SingleCellExperiment)
21 23 
 import(ape)
... ... 
@@ -27,6 +29,7 @@ import(ggplot2)
27 29 
 import(kernlab, except = c(alpha, predict))
28 30 
 import(methods)
29 31 
 import(pROC)
32 
+import(tools)
30 33 
 importFrom(Seurat,GetAssayData)
31 34 
 importFrom(SummarizedExperiment,assay)
32 35 
 importFrom(SummarizedExperiment,colData)
Browse code

reduce duplication code in train_classifier and test_classifier remove parameter signature in support functions

Former-commit-id: 81d3b0fe59b49b602a776ff4e086660b05ead3b0

nttvy authored on 28/07/2021 23:43:14
Showing 1 changed files
NAMESPACE
History View file @ b867bca
... ... 
@@ -28,8 +28,6 @@ import(kernlab, except = c(alpha, predict))
28 28 
 import(methods)
29 29 
 import(pROC)
30 30 
 importFrom(Seurat,GetAssayData)
31 
-importFrom(Seurat,Idents)
32 
-importFrom(SingleCellExperiment,colData)
33 31 
 importFrom(SummarizedExperiment,assay)
34 32 
 importFrom(SummarizedExperiment,colData)
35 33 
 importFrom(stats,predict)
Browse code

replace core clf by caret_model replace all other clf by classifiers

Former-commit-id: 91ec8da24f45c110ab4f2e728ab71e9c1d255ca8

nttvy authored on 22/07/2021 13:51:48
Showing 1 changed files
NAMESPACE
History View file @ adb6f19
... ... 
@@ -2,9 +2,9 @@
2 2
3 3 
 export("cell_type<-")
4 4 
 export("p_thres<-")
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+export(caret_model)
5 6 
 export(cell_type)
6 7 
 export(classify_cells)
7 
-export(clf)
8 8 
 export(delete_model)
9 9 
 export(marker_genes)
10 10 
 export(p_thres)
Browse code

change features to marker_genes

Former-commit-id: b8f82581ead9bfe31c088db02857a1d1c996d832

nttvy authored on 22/07/2021 11:32:05
Showing 1 changed files
NAMESPACE
History View file @ 7e9ee09
... ... 
@@ -6,7 +6,7 @@ export(cell_type)
6 6 
 export(classify_cells)
7 7 
 export(clf)
8 8 
 export(delete_model)
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-export(features)
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+export(marker_genes)
10 10 
 export(p_thres)
11 11 
 export(parent)
12 12 
 export(plant_tree)
Browse code

rename package from scClassifR to scAnnotatR

Former-commit-id: 9823f9b8cf0ad38ebbe2bcd6f870a63a98c29d07

nttvy authored on 01/07/2021 12:02:51
Showing 1 changed files
NAMESPACE
History View file @ 499496a
... ... 
@@ -12,7 +12,7 @@ export(parent)
12 12 
 export(plant_tree)
13 13 
 export(plot_roc_curve)
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 export(save_new_model)
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-export(scClassifR)
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+export(scAnnotatR)
16 16 
 export(test_classifier)
17 17 
 export(train_classifier)
18 18 
 exportMethods(show)
Browse code

fix bug in cluster prediction: duplication in cluster prediction generates error

Former-commit-id: 177d9b7784ebafa7762070d8617c6d3ea022be1c

nttvy authored on 19/04/2021 22:15:47
Showing 1 changed files
NAMESPACE
History View file @ 7dfeff6
... ... 
@@ -32,7 +32,6 @@ importFrom(Seurat,Idents)
32 32 
 importFrom(SingleCellExperiment,colData)
33 33 
 importFrom(SummarizedExperiment,assay)
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 importFrom(SummarizedExperiment,colData)
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-importFrom(plyr,mapvalues)
36 35 
 importFrom(stats,predict)
37 36 
 importFrom(stats,sd)
38 37 
 importFrom(stats,setNames)
Browse code

add cluster prediction

Former-commit-id: 685a1adef1ea382464e57dc19fad76eac8355ea0

nttvy authored on 10/04/2021 17:44:04
Showing 1 changed files
NAMESPACE
History View file @ 6c63e3c
... ... 
@@ -32,6 +32,7 @@ importFrom(Seurat,Idents)
32 32 
 importFrom(SingleCellExperiment,colData)
33 33 
 importFrom(SummarizedExperiment,assay)
34 34 
 importFrom(SummarizedExperiment,colData)
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+importFrom(plyr,mapvalues)
35 36 
 importFrom(stats,predict)
36 37 
 importFrom(stats,sd)
37 38 
 importFrom(stats,setNames)
Browse code

rename package

Former-commit-id: c41bda4739a20cb0a346da77aaa02256d756b67f

nttvy authored on 29/12/2020 00:49:20
Showing 1 changed files
NAMESPACE
History View file @ 0ed9c39
... ... 
@@ -12,6 +12,7 @@ export(parent)
12 12 
 export(plant_tree)
13 13 
 export(plot_roc_curve)
14 14 
 export(save_new_model)
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+export(scClassifR)
15 16 
 export(test_classifier)
16 17 
 export(train_classifier)
17 18 
 exportMethods(show)
Browse code

use accessors instead of @

Former-commit-id: 5c273ba5e13fb4ff1f33f38f231694df7f600074

nttvy authored on 22/12/2020 22:05:24
Showing 1 changed files
NAMESPACE
History View file @ 7e29eda
... ... 
@@ -27,6 +27,7 @@ import(kernlab, except = c(alpha, predict))
27 27 
 import(methods)
28 28 
 import(pROC)
29 29 
 importFrom(Seurat,GetAssayData)
30 
+importFrom(Seurat,Idents)
30 31 
 importFrom(SingleCellExperiment,colData)
31 32 
 importFrom(SummarizedExperiment,assay)
32 33 
 importFrom(SummarizedExperiment,colData)
Browse code

group non exported functions

Former-commit-id: 6c0f23354428e151ce50a784d61b6a9bcad0861a

nttvy authored on 22/12/2020 16:30:32
Showing 1 changed files
NAMESPACE
History View file @ 34c7392
... ... 
@@ -12,7 +12,6 @@ export(parent)
12 12 
 export(plant_tree)
13 13 
 export(plot_roc_curve)
14 14 
 export(save_new_model)
15 
-export(scTypeR)
16 15 
 export(test_classifier)
17 16 
 export(train_classifier)
18 17 
 exportMethods(show)
Browse code

add data.tree to namespace

Former-commit-id: d86b6b60f26f1caaf24cf50516787d5ec3494c99

nttvy authored on 15/12/2020 12:57:29
Showing 1 changed files
NAMESPACE
History View file @ 94e3aed
... ... 
@@ -20,6 +20,7 @@ import(ROCR)
20 20 
 import(SingleCellExperiment)
21 21 
 import(ape)
22 22 
 import(caret)
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+import(data.tree)
23 24 
 import(dplyr)
24 25 
 import(e1071)
25 26 
 import(ggplot2)
Browse code

move default models to new package

Former-commit-id: 19cd06664bb8f459cf8f8d6dc6b80320c0ba91ea

nttvy authored on 01/12/2020 12:05:05
Showing 1 changed files
NAMESPACE
History View file @ 4a399bf
... ... 
@@ -12,6 +12,7 @@ export(parent)
12 12 
 export(plant_tree)
13 13 
 export(plot_roc_curve)
14 14 
 export(save_new_model)
15 
+export(scTypeR)
15 16 
 export(test_classifier)
16 17 
 export(train_classifier)
17 18 
 exportMethods(show)
Browse code

merge plant_tree & visualize_tree to only plant_tree, remove mouse models

Former-commit-id: 8efa5767ef98d0619d918fdab9e7f24902d7b24a

nttvy authored on 26/11/2020 11:54:20
Showing 1 changed files
NAMESPACE
History View file @ 4d990d8
... ... 
@@ -14,13 +14,11 @@ export(plot_roc_curve)
14 14 
 export(save_new_model)
15 15 
 export(test_classifier)
16 16 
 export(train_classifier)
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-export(visualize_tree)
18 17 
 exportMethods(show)
19 18 
 import(ROCR)
20 19 
 import(SingleCellExperiment)
21 20 
 import(ape)
22 21 
 import(caret)
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-import(data.tree)
24 22 
 import(dplyr)
25 23 
 import(e1071)
26 24 
 import(ggplot2)
Browse code

Initial commit

Former-commit-id: c30d5e0eb17749597b12316855f05517b93b7be9

Johannes Griss authored on 10/11/2020 10:34:39
Showing 1 changed files
NAMESPACE
History View file @ 0065b78
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,37 @@
1 
+# Generated by roxygen2: do not edit by hand
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+
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+export("cell_type<-")
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+export("p_thres<-")
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+export(cell_type)
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+export(classify_cells)
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+export(clf)
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+export(delete_model)
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+export(features)
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+export(p_thres)
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+export(parent)
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+export(plant_tree)
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+export(plot_roc_curve)
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+export(save_new_model)
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+export(test_classifier)
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+export(train_classifier)
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+export(visualize_tree)
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+exportMethods(show)
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+import(ROCR)
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+import(SingleCellExperiment)
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+import(ape)
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+import(caret)
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+import(data.tree)
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+import(dplyr)
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+import(e1071)
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+import(ggplot2)
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+import(kernlab, except = c(alpha, predict))
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+import(methods)
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+import(pROC)
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+importFrom(Seurat,GetAssayData)
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+importFrom(SingleCellExperiment,colData)
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+importFrom(SummarizedExperiment,assay)
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+importFrom(SummarizedExperiment,colData)
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+importFrom(stats,predict)
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+importFrom(stats,sd)
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+importFrom(stats,setNames)
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+importFrom(utils,data)